add recommendations in README

kkang7 · May 3, 2021 · 8232fdc · 8232fdc
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diff --git a/README.Rmd b/README.Rmd
@@ -108,6 +108,18 @@ cdseq.result.celltypeassign <- cellTypeAssignSCRNA(cdseq_gep = cdseq.result$estG
                                                    plot_tsne = 0)
 ```
 
+## Setting recommendations
+We provide recommendations for parameter settings. Note that these recommendations are merely emperical and there is no theoretical justifications yet. User can tune the parameters based on specific applications and domain knowledges. 
+
+Parameters      Recommended setting
+--------------- ----------------------
+beta            0.5
+alpha           5
+mcmc_iteration   700-2000
+dilution_factor   2-10
+gene_subset_size  200-500
+block_number      >5
+
 Check vignette for more details and examples: *browseVignettes("CDSeq")*.
 
 ## Contact 

diff --git a/README.md b/README.md
@@ -122,6 +122,22 @@ cdseq.result.celltypeassign <- cellTypeAssignSCRNA(cdseq_gep = cdseq.result$estG
                                                    plot_tsne = 0)
 ```
 
+## Setting recommendations
+
+We provide recommendations for parameter settings. Note that these
+recommendations are merely emperical and there is no theoretical
+justifications yet. User can tune the parameters based on specific
+applications and domain knowledges.
+
+| Parameters         | Recommended setting |
+| :----------------- | :------------------ |
+| beta               | 0.5                 |
+| alpha              | 5                   |
+| mcmc\_iteration    | 700-2000            |
+| dilution\_factor   | 2-10                |
+| gene\_subset\_size | 200-500             |
+| block\_number      | \>5                 |
+
 Check vignette for more details and examples:
 *browseVignettes(“CDSeq”)*.